TY - JOUR A1 - Vohra, Sumit Kumar A1 - Herrera, Kristian A1 - Tavhelidse-Suck, Tinatini A1 - Knoblich, Simon A1 - Seleit, Ali A1 - Boulanger-Weill, Jonathan A1 - Chambule, Sydney A1 - Aspiras, Ariel A1 - Santoriello, Cristina A1 - Randlett, Owen A1 - Wittbrodt, Joachim A1 - Aulehla, Alexander A1 - Lichtman, Jeff W. A1 - Fishman, Mark A1 - Hege, Hans-Christian A1 - Baum, Daniel A1 - Engert, Florian A1 - Isoe, Yasuko T1 - Multi-species community platform for comparative neuroscience in teleost fish JF - bioRxiv N2 - Studying neural mechanisms in complementary model organisms from different ecological niches in the same animal class can leverage the comparative brain analysis at the cellular level. To advance such a direction, we developed a unified brain atlas platform and specialized tools that allowed us to quantitatively compare neural structures in two teleost larvae, medaka (Oryzias latipes) and zebrafish (Danio rerio). Leveraging this quantitative approach we found that most brain regions are similar but some subpopulations are unique in each species. Specifically, we confirmed the existence of a clear dorsal pallial region in the telencephalon in medaka lacking in zebrafish. Further, our approach allows for extraction of differentially expressed genes in both species, and for quantitative comparison of neural activity at cellular resolution. The web-based and interactive nature of this atlas platform will facilitate the teleost community’s research and its easy extensibility will encourage contributions to its continuous expansion. Y1 - 2024 U6 - https://doi.org/10.1101/2024.02.14.580400 ER - TY - GEN A1 - Hajarolasvadi, Noushin A1 - Baum, Daniel T1 - Data for Training the DeepOrientation Model: Simulated cryo-ET tomogram patches N2 - A major restriction to applying deep learning methods in cryo-electron tomography is the lack of annotated data. Many large learning-based models cannot be applied to these images due to the lack of adequate experimental ground truth. One appealing alternative solution to the time-consuming and expensive experimental data acquisition and annotation is the generation of simulated cryo-ET images. In this context, we exploit a public cryo-ET simulator called PolNet to generate three datasets of two macromolecular structures, namely the ribosomal complex 4v4r and Thermoplasma acidophilum 20S proteasome, 3j9i. We select these two specific particles to test whether our models work for macromolecular structures with and without rotational symmetry. The three datasets contain 50, 150, and 450 tomograms with a voxel size of 10 ̊A, respectively. Here, we publish patches of size 40 × 40 × 40 extracted from the medium-sized dataset with 26,703 samples of 4v4r and 40,671 samples of 3j9i. The original tomograms from which the samples were extracted are of size 500 × 500 × 250. Finally, it should be noted that the currently published test dataset is employed for reporting the results of our paper titled ”DeepOrientation: Deep Orientation Estimation of Macromolecules in Cryo-electron tomography” paper. Y1 - 2024 U6 - https://doi.org/10.12752/9686 ER - TY - JOUR A1 - Yang, Binru A1 - Knötel, David A1 - Ciecierska-Holmes, Jana A1 - Wölfer, Jan A1 - Chaumel, Júlia A1 - Zaslansky, Paul A1 - Baum, Daniel A1 - Fratzl, Peter A1 - Dean, Mason N. T1 - Growth of a tessellation: geometric rules for the development of stingray skeletal patterns JF - Advanced Science Y1 - 2024 U6 - https://doi.org/10.1002/advs.202407641 VL - 11 IS - 48 ER - TY - JOUR A1 - Eigen, Lennart A1 - Wölfer, Jan A1 - Baum, Daniel A1 - Van Le, Mai-Lee A1 - Werner, Daniel A1 - Dean, Mason N. A1 - Nyakatura, John A. T1 - Comparative architecture of the tessellated boxfish (Ostracioidea) carapace JF - Communications Biology Y1 - 2024 U6 - https://doi.org/10.1038/s42003-024-07119-z VL - 7 ER - TY - JOUR A1 - Mayer, Julius A1 - Baum, Daniel A1 - Ambellan, Felix A1 - von Tycowicz, Christoph A1 - for the Alzheimer’s Disease Neuroimaging Initiative, T1 - Shape-based Disease Grading via Functional Maps and Graph Convolutional Networks with Application to Alzheimer’s Disease JF - BMC Medical Imaging N2 - Shape analysis provides methods for understanding anatomical structures extracted from medical images. However, the underlying notions of shape spaces that are frequently employed come with strict assumptions prohibiting the analysis of incomplete and/or topologically varying shapes. This work aims to alleviate these limitations by adapting the concept of functional maps. Further, we present a graph-based learning approach for morphometric classification of disease states that uses novel shape descriptors based on this concept. We demonstrate the performance of the derived classifier on the open-access ADNI database differentiating normal controls and subjects with Alzheimer’s disease. Notably, the experiments show that our approach can improve over state-of-the-art from geometric deep learning. Y1 - 2024 U6 - https://doi.org/10.1186/s12880-024-01513-z VL - 24 ER - TY - CHAP A1 - Gossing, Anne A1 - Beckert, Andreas A1 - Fischer, Christoph A1 - Klenert, Nicolas A1 - Natarajan, Vijay A1 - Pacey, George A1 - Vogt, Thorwin A1 - Rautenhaus, Marc A1 - Baum, Daniel T1 - A Ridge-based Approach for Extraction and Visualization of 3D Atmospheric Fronts T2 - 2024 IEEE Visualization and Visual Analytics (VIS) N2 - An atmospheric front is an imaginary surface that separates two distinct air masses and is commonly defined as the warm-air side of a frontal zone with high gradients of atmospheric temperature and humidity. These fronts are a widely used conceptual model in meteorology, which are often encountered in the literature as two-dimensional (2D) front lines on surface analysis charts. This paper presents a method for computing three-dimensional (3D) atmospheric fronts as surfaces that is capable of extracting continuous and well-confined features suitable for 3D visual analysis, spatio-temporal tracking, and statistical analyses. Recently developed contour-based methods for 3D front extraction rely on computing the third derivative of a moist potential temperature field. Additionally, they require the field to be smoothed to obtain continuous large-scale structures. This paper demonstrates the feasibility of an alternative method to front extraction using ridge surface computation. The proposed method requires only the sec- ond derivative of the input field and produces accurate structures even from unsmoothed data. An application of the ridge-based method to a data set corresponding to Cyclone Friederike demonstrates its benefits and utility towards visual analysis of the full 3D structure of fronts. Y1 - 2024 U6 - https://doi.org/10.1109/VIS55277.2024.00043 SP - 176 EP - 180 ER - TY - JOUR A1 - Harth, Philipp A1 - Udvary, Daniel A1 - Boelts, Jan A1 - Baum, Daniel A1 - Macke, Jakob H. A1 - Hege, Hans-Christian A1 - Oberlaender, Marcel T1 - Dissecting origins of wiring specificity in dense cortical connectomes JF - bioRxiv N2 - Wiring specificity in the cortex is observed across scales from the subcellular to the network level. It describes the deviations of connectivity patterns from those expected in randomly connected networks. Understanding the origins of wiring specificity in neural networks remains difficult as a variety of generative mechanisms could have contributed to the observed connectome. To take a step forward, we propose a generative modeling framework that operates directly on dense connectome data as provided by saturated reconstructions of neural tissue. The computational framework allows testing different assumptions of synaptic specificity while accounting for anatomical constraints posed by neuron morphology, which is a known confounding source of wiring specificity. We evaluated the framework on dense reconstructions of the mouse visual and the human temporal cortex. Our template model incorporates assumptions of synaptic specificity based on cell type, single-cell identity, and subcellular compartment. Combinations of these assumptions were sufficient to model various connectivity patterns that are indicative of wiring specificity. Moreover, the identified synaptic specificity parameters showed interesting similarities between both datasets, motivating further analysis of wiring specificity across species. Y1 - 2024 U6 - https://doi.org/10.1101/2024.12.14.628490 ER - TY - JOUR A1 - Klenert, Nicolas A1 - Lepper, Verena A1 - Baum, Daniel T1 - A Local Iterative Approach for the Extraction of 2D Manifolds from Strongly Curved and Folded Thin-Layer Structures JF - IEEE Transactions on Visualization and Computer Graphics N2 - Ridge surfaces represent important features for the analysis of 3-dimensional (3D) datasets in diverse applications and are often derived from varying underlying data including flow fields, geological fault data, and point data, but they can also be present in the original scalar images acquired using a plethora of imaging techniques. Our work is motivated by the analysis of image data acquired using micro-computed tomography (μCT) of ancient, rolled and folded thin-layer structures such as papyrus, parchment, and paper as well as silver and lead sheets. From these documents we know that they are 2-dimensional (2D) in nature. Hence, we are particularly interested in reconstructing 2D manifolds that approximate the document’s structure. The image data from which we want to reconstruct the 2D manifolds are often very noisy and represent folded, densely-layered structures with many artifacts, such as ruptures or layer splitting and merging. Previous ridge-surface extraction methods fail to extract the desired 2D manifold for such challenging data. We have therefore developed a novel method to extract 2D manifolds. The proposed method uses a local fast marching scheme in combination with a separation of the region covered by fast marching into two sub-regions. The 2D manifold of interest is then extracted as the surface separating the two sub-regions. The local scheme can be applied for both automatic propagation as well as interactive analysis. We demonstrate the applicability and robustness of our method on both artificial data as well as real-world data including folded silver and papyrus sheets. Y1 - 2024 U6 - https://doi.org/10.1109/TVCG.2023.3327403 VL - 30 IS - 1 SP - 1260 EP - 1270 ER - TY - JOUR A1 - Vohra, Sumit Kumar A1 - Harth, Philipp A1 - Isoe, Yasuko A1 - Bahl, Armin A1 - Fotowat, Haleh A1 - Engert, Florian A1 - Hege, Hans-Christian A1 - Baum, Daniel T1 - A Visual Interface for Exploring Hypotheses about Neural Circuits JF - IEEE Transactions on Visualization and Computer Graphics N2 - One of the fundamental problems in neurobiological research is to understand how neural circuits generate behaviors in response to sensory stimuli. Elucidating such neural circuits requires anatomical and functional information about the neurons that are active during the processing of the sensory information and generation of the respective response, as well as an identification of the connections between these neurons. With modern imaging techniques, both morphological properties of individual neurons as well as functional information related to sensory processing, information integration and behavior can be obtained. Given the resulting information, neurobiologists are faced with the task of identifying the anatomical structures down to individual neurons that are linked to the studied behavior and the processing of the respective sensory stimuli. Here, we present a novel interactive tool that assists neurobiologists in the aforementioned task by allowing them to extract hypothetical neural circuits constrained by anatomical and functional data. Our approach is based on two types of structural data: brain regions that are anatomically or functionally defined, and morphologies of individual neurons. Both types of structural data are interlinked and augmented with additional information. The presented tool allows the expert user to identify neurons using Boolean queries. The interactive formulation of these queries is supported by linked views, using, among other things, two novel 2D abstractions of neural circuits. The approach was validated in two case studies investigating the neural basis of vision-based behavioral responses in zebrafish larvae. Despite this particular application, we believe that the presented tool will be of general interest for exploring hypotheses about neural circuits in other species, genera and taxa. Y1 - 2024 U6 - https://doi.org/10.1109/TVCG.2023.3243668 VL - 30 IS - 7 SP - 3945 EP - 3958 ER - TY - JOUR A1 - Lützkendorf, Janine A1 - Matkovic-Rachid, Tanja A1 - Liu, Sunbin A1 - Götz, Torsten A1 - Gao, Lili A1 - Turrel, Oriane A1 - Maglione, Marta A1 - Grieger, Melanie A1 - Putignano, Sabrina A1 - Ramesh, Niraja A1 - Ghelani, Tina A1 - Neumann, Alexander A1 - Gimber, Niclas A1 - Schmoranzer, Jan A1 - Stawrakakis, Anastasia A1 - Brence, Blaž A1 - Baum, Daniel A1 - Ludwig, Kai A1 - Heine, Martin A1 - Mielke, Thorsten A1 - Liu, Fan A1 - Walter, Alexander A1 - Wahl, Markus A1 - Sigrist, Stephan T1 - Blobby is a synaptic active zone assembly protein required for memory in Drosophila JF - Nature Communications Y1 - 2025 U6 - https://doi.org/10.1038/s41467-024-55382-9 VL - 16 ER - TY - CHAP A1 - Klenert, Nicolas A1 - Schwoerer, Finn A1 - Hajarolasvadi, Noushin A1 - Bournez, Siloé A1 - Arlt, Tobias A1 - Mahnke, Heinz-Eberhard A1 - Lepper, Verena A1 - Baum, Daniel T1 - Improving the Identification of Layers in 3D Images of Ancient Papyrus using Artificial Neural Networks T2 - 2025 IEEE/CVF Winter Conference on Applications of Computer Vision Workshops (WACVW), Tucson, AZ, USA N2 - The process of digitally unfolding ancient documents, such as folded papyrus packages, from 3D image data aims to be a non-invasive means to make previously hidden writing visible without risking to damage the precious documents. One of the main tasks necessary to digitally unfold a document is the geometric reconstruction of the writing substrate, which is a prerequisite for its subsequent unfolding. All current reconstruction methods require the existence of an interspace between different layers of the document to ensure a correct topology. Layers that appear merged together in the 3D image often result in wrong connections between layers and thus also in a wrong topology of the reconstructed geometry, which hinders the successful unfolding. Here, we propose to use a neural network to facilitate the discrimination of the layers. Using papyrus documents as an example of a particularly difficult writing material, we show that this significantly reduces the number of wrong connections and improves the overall identification of the layers. This in turn enables fully automatic digital unfolding of large areas of highly complex papyrus packages. Utilizing explainable AI (XAI) further allows us to explore the results of the applied neural network. Y1 - 2025 U6 - https://doi.org/10.1109/WACVW65960.2025.00143 SP - 1204 EP - 1212 ER - TY - JOUR A1 - Boulanger-Weill, Jonathan A1 - Kaempf, Florian A1 - L. Schalek, Richard A1 - Petkova, Mariela A1 - Vohra, Sumit Kumar A1 - Savaliya, Jay H. A1 - Wu, Yuelong A1 - Schuhknecht, Gregor F. P. A1 - Naumann, Heike A1 - Eberle, Maren A1 - Kirchberger, Kim N. A1 - Rencken, Simone A1 - Bianco, Isaac H. A1 - Baum, Daniel A1 - Bene, Filippo Del A1 - Engert, Florian A1 - Lichtman, Jeff W. A1 - Bahl, Armin T1 - Correlative light and electron microscopy reveals the fine circuit structure underlying evidence accumulation in larval zebrafish JF - bioRxiv N2 - Accumulating information is a critical component of most circuit computations in the brain across species, yet its precise implementation at the synaptic level remains poorly understood. Dissecting such neural circuits in vertebrates requires precise knowledge of functional neural properties and the ability to directly correlate neural dynamics with the underlying wiring diagram in the same animal. Here we combine functional calcium imaging with ultrastructural circuit reconstruction, using a visual motion accumulation paradigm in larval zebrafish. Using connectomic analyses of functionally identified cells and computational modeling, we show that bilateral inhibition, disinhibition, and recurrent connectivity are prominent motifs for sensory accumulation within the anterior hindbrain. We also demonstrate that similar insights about the structure-function relationship within this circuit can be obtained through complementary methods involving cell-specific morphological labeling via photo-conversion of functionally identified neuronal response types. We used our unique ground truth datasets to train and test a novel classifier algorithm, allowing us to assign functional labels to neurons from morphological libraries where functional information is lacking. The resulting feature-rich library of neuronal identities and connectomes enabled us to constrain a biophysically realistic network model of the anterior hindbrain that can reproduce observed neuronal dynamics and make testable predictions for future experiments. Our work exemplifies the power of hypothesis-driven electron microscopy paired with functional recordings to gain mechanistic insights into signal processing and provides a framework for dissecting neural computations across vertebrates. Y1 - 2025 U6 - https://doi.org/10.1101/2025.03.14.643363 ER - TY - JOUR A1 - Li, Tairan A1 - Schindler, Mike A1 - Paskin, Martha A1 - Surapaneni, Venkata A. A1 - Scott, Elliott A1 - Hauert, Sabine A1 - Payne, Nicholas A1 - Cade, David E. A1 - Goldbogen, Jeremy A. A1 - Mollen, Frederik H. A1 - Baum, Daniel A1 - Hanna, Sean A1 - Dean, Mason N. T1 - Functional models from limited data: a parametric and multimodal approach to anatomy and 3D kinematics of feeding in basking sharks (Cetorhinus maximus) JF - The Anatomical Record Y1 - 2025 U6 - https://doi.org/10.1002/ar.25693 ER - TY - CHAP A1 - Brence, Blaž A1 - Fuchs, Joachim A1 - Hiesinger, Peter Robin A1 - Baum, Daniel ED - Garrison, Laura ED - Krueger, Robert T1 - Fully automated quantification of synaptic locations in multi-channel Drosophila photoreceptor microscopy data T2 - Eurographics Workshop on Visual Computing for Biology and Medicine N2 - The workload posed by image analysis remains a major bottleneck for advances across the life sciences. To address this challenge, we have developed a fully automated workflow for processing complex 3D multi-channel microscopy images. Specifically, our workflow addresses the analysis of photoreceptor synapses in confocal images of the Drosophila melanogaster optic lobe. The workflow consists of multiple stages, combining traditional and machine learning–based approaches for image analysis and visual computing. It performs segmentation of brain regions, photoreceptor instance identification, and precise localization of synapses. The key novelty of the workflow is an automatic alignment of synapses into a cylindrical reference coordinate system, enabling comparative synaptic analysis across photoreceptors. To demonstrate the workflow’s applicability, preliminary biological results and their interpretation based on 50 images are presented. While the workflow is still being improved further, here, we showcase its capacity for efficient and objective data processing for high-throughput neurobiological analyses. Y1 - 2025 U6 - https://doi.org/10.2312/vcbm.20251254 ER - TY - JOUR A1 - Vohra, Sumit Kumar A1 - Eberle, Maren A1 - Boulanger-Weill, Jonathan A1 - Petkova, Mariela D. A1 - Schuhknecht, Gregor F. P. A1 - Herrera, Kristian J. A1 - Kämpf, Florian A1 - Ruetten, Virginia M. S. A1 - Lichtman, Jeff W. A1 - Engert, Florian A1 - Randlett, Owen A1 - Bahl, Armin A1 - Isoe, Yasuko A1 - Hege, Hans-Christian A1 - Baum, Daniel T1 - Fishexplorer: A multimodal cellular atlas platform for neuronal circuit dissection in larval zebrafish JF - bioRxiv N2 - Understanding how neural circuits give rise to behavior requires comprehensive knowledge of neuronal morphology, connectivity, and function. Atlas platforms play a critical role in enabling the visualization, exploration, and dissemination of such information. Here, we present FishExplorer, an interactive and expandable community platform designed to integrate and analyze multimodal brain data from larval zebrafish. FishExplorer supports datasets acquired through light microscopy (LM), electron microscopy (EM), and X-ray imaging, all co-registered within a unified spatial coordinate system which enables seamless comparison of neuronal morphologies and synaptic connections. To further assist circuit analysis, FishExplorer includes a suite of tools for querying and visualizing connectivity at the whole-brain scale. By integrating data from recent large-scale EM reconstructions (presented in companion studies), FishExplorer enables researchers to validate circuit models, explore wiring principles, and generate new hypotheses. As a continuously evolving resource, FishExplorer is designed to facilitate collaborative discovery and serve the growing needs of the teleost neuroscience community. Y1 - 2025 U6 - https://doi.org/10.1101/2025.07.14.664689 ER - TY - JOUR A1 - Okafornta, Chukwuebuka William A1 - Farhadifar, Reza A1 - Fabig, Gunar A1 - Wu, Hai-Yin A1 - Köckert, Maria A1 - Vogel, Martin A1 - Baum, Daniel A1 - Haase, Robert A1 - Shelley, Michael J. A1 - Needleman, Daniel J. A1 - Müller-Reichert, Thomas T1 - Cell size reduction scales spindle elongation but not chromosome segregation in C. elegans JF - bioRxiv N2 - How embryos adapt their internal cellular machinery to reductions in cell size during development remains a fundamental question in cell biology. Here, we use high-resolution lattice light-sheet fluorescence microscopy and automated image analysis to quantify lineage-resolved mitotic spindle and chromosome segregation dynamics from the 2– to 64–cell stages in Caenorhabditis elegans embryos. While spindle length scales with cell size across both wild-type and size-perturbed embryos, chromosome segregation dynamics remain largely invariant, suggesting that distinct mechanisms govern these mitotic processes. Combining femtosecond laser ablation with large-scale electron tomography, we find that central spindle microtubules mediate chromosome segregation dynamics and remain uncoupled from cell size across all stages of early development. In contrast, spindle elongation is driven by cortically anchored motor proteins and astral microtubules, rendering it sensitive to cell size. Incorporating these experimental results into an extended stoichiometric model for both the spindle and chromosomes, we find that allowing only cell size and microtubule catastrophe rates to vary reproduces elongation dynamics across development. The same model also accounts for centrosome separation and pronuclear positioning in the one-cell C. elegans embryo, spindle-length scaling across nematode species spanning ~100 million years of divergence, and spindle rotation in human cells. Thus, a unified stoichiometric framework provides a predictive, mechanistic account of spindle and nuclear dynamics across scales and species. Y1 - 2025 U6 - https://doi.org/10.1101/2025.10.13.681585 ER - TY - JOUR A1 - Hu, Chenhao A1 - Tutika, Ravi A1 - Deng, Zhifei A1 - Jia, Zian A1 - Chen, Liuni A1 - Chen, Hongshun A1 - Geng, Yang A1 - Xiao, Xianghui A1 - Shevchenko, Pavel D. A1 - Pierre, Christoph A1 - Weaver, James C. A1 - Baum, Daniel A1 - Bartlett, Michael D. A1 - Li, Ling T1 - Mineralized sclerites in the gorgonian coral Leptogorgia chilensis as a natural jamming system JF - PNAS Y1 - 2025 U6 - https://doi.org/10.1073/pnas.2504541122 VL - 122 IS - 44 ER - TY - JOUR A1 - Sterzik, Anna A1 - Krone, Michael A1 - Baum, Daniel A1 - Cunningham, Douglas W. A1 - Lawonn, Kai T1 - Uncertainty Visualization for Biomolecular Structures: An Empirical Evaluation JF - IEEE Transactions on Visualization and Computer Graphics N2 - Uncertainty is an intrinsic property of almost all data, regardless of the data being measured, simulated, or generated. It can significantly influence the results and reliability of subsequent analysis steps. Clearly communicating uncertainties is crucial for informed decision-making and understanding, especially in biomolecular data, where uncertainty is often difficult to infer. Uncertainty visualization (UV) is a powerful tool for this purpose. However, previously proposed UV methods lack sufficient empirical evaluation. We collected and categorized visualization methods for portraying positional uncertainty in biomolecular structures. We then organized the methods into metaphorical groups and extracted nine representatives: color, clouds, ensemble, hulls, sausages, contours, texture, waves, and noise. We assessed their strengths and weaknesses in a twofold approach: expert assessments with six domain experts and three perceptual evaluations involving 1,756 participants. Through the expert assessments, we aimed to highlight the advantages and limitations of the individual methods for the application domain and discussed areas for necessary improvements. Through the perceptual evaluation, we investigated whether the visualizations are intuitively associated with uncertainty and whether the directionality of the mapping is perceived as intended. We also assessed the accuracy of inferring uncertainty values from the visualizations. Based on our results, we judged the appropriateness of the metaphors for encoding uncertainty and suggest further areas for improvement. Y1 - 2025 U6 - https://doi.org/10.1109/TVCG.2025.3596385 VL - 31 IS - 12 SP - 10296 EP - 10310 ER - TY - JOUR A1 - Eigen, Lennart A1 - Ladenburger, Pius A1 - Brence, Blaž A1 - Shubitidze, Ani A1 - Baum, Daniel A1 - Hildebrandt, Thomas A1 - Brecht, Michael T1 - Elephant trunk tip musculature reflects species differences in grasping behavior JF - Communications Biology N2 - Elephants use their trunks, muscular hydrostats, to perform a plethora of tasks. Trunk tip morphology as well as grasping behavior differ between elephant species. While African savanna elephants (Loxodonta africana) use their dorsal and ventral finger for pinching movements, Asian elephants (Elephas maximus) prefer to wrap around objects with their one dorsal finger and ventral bulb trunk tip lip. Moreover, E. maximus can flip their ventral bulb backwards to clamp objects behind the trunk tip. Whether trunk tip musculature differs between elephant species and muscle architecture is reflected by preferred grasping behavior is, however, not clear. In this study, we performed dense muscle fascicle reconstruction of three L. africana and three E. maximus hemi-trunk tips using a combination of manual and automated segmentation of high-resolution microfocus tomography (microCT) scans. We distinguish three types of muscle fascicles: longitudinal (bending and shortening), radial (elongating) and transversal muscle fascicles (elongating). We found that trunk tips of L. africana consist to one third of longitudinal and two thirds radial/transversal muscle fascicles, likely aiding in their grasping behavior, while E. maximus trunk tips consist to two thirds of longitudinal and one third radial/transversal muscle fascicles, which is advantageous for their wrapping and backward clamping behavior. Y1 - 2025 U6 - https://doi.org/10.1038/s42003-025-08998-6 VL - 8 ER - TY - JOUR A1 - Schmitt, Kira A1 - Titschack, Jürgen A1 - Baum, Daniel T1 - CoDA: Interactive Segmentation and Morphological Analysis of Dendroid Structures Exemplified on Stony Cold-Water Corals JF - IEEE Transactions on Visualization and Computer Graphics Y1 - 2026 U6 - https://doi.org/10.1109/TVCG.2026.3656066 ER - TY - JOUR A1 - Brence, Blaž A1 - Brummer, Josephine A1 - Dercksen, Vincent J. A1 - Özel, Mehmet Neset A1 - Kulkarni, Abhishkek A1 - Wolterhoff, Neele A1 - Prohaska, Steffen A1 - Hiesinger, Peter Robin A1 - Baum, Daniel T1 - Semi-automatic Geometrical Reconstruction and Analysis of Filopodia Dynamics in 4D Two-Photon Microscopy Images JF - bioRxiv N2 - Background: Filopodia are thin and dynamic membrane protrusions that play a crucial role in cell migration, axon guidance, and other processes where cells explore and interact with their surroundings. Historically, filopodial dynamics have been studied in great detail in 2D in cultured cells, and more recently in 3D culture as well as living brains. However, there is a lack of efficient tools to trace and track filopodia in 4D images of complex brain cells. Results: To address this issue, we have developed a semi-automatic workflow for tracing filopodia in 3D images and tracking the traced filopodia over time. The workflow was developed based on high-resolution data of photoreceptor axon terminals in the in vivo context of normal Drosophila brain development, but devised to be applicable to filopodia in any system, including at different temporal and spatial scales. In contrast to the pre-existing methods, our workflow relies solely on the original intensity images without the requirement for segmentation or complex preprocessing. The workflow was realized in C++ within the Amira software system and consists of two main parts, dataset pre-processing, and geometrical filopodia reconstruction, where each of the two parts comprises multiple steps. In this paper, we provide an extensive workflow description and demonstrate its versatility for two different axo-dendritic morphologies, R7 and Dm8 cells. Finally, we provide an analysis of the time requirements for user input and data processing. Conclusion: To facilitate simple application within Amira or other frameworks, we share the source code, which is available athttps://github.com/zibamira/filopodia-tool. Y1 - 2025 U6 - https://doi.org/10.1101/2025.05.20.654789 ER - TY - JOUR A1 - Brence, Blaž A1 - Wandelt, Laura R. A1 - Walter, Sophie A1 - Sigrist, Stephan J. A1 - Petzoldt, Astrid G. A1 - Baum, Daniel T1 - Semi-automatic 3D-quantification of in-vivo synapse formation JF - ResearchSquare N2 - Background: Synapses, as specialised cell-cell contacts, allow for a faithful and controlled signal transmission between a neuron and a target cell. Presynapses, the sites of neurotransmitter release, form de novo throughout the development of an organism. Although this process is fundamental to the development and function of synaptic circuits, how developing neurons control number and distribution of individual synapses remains poorly understood. In-vivo imaging analysis of synapse formation at the neuromuscular junction of anaesthetised Drosophila third instar larvae allows for spatial and temporal resolution of the underlying molecular processes. However, high-throughput, comprehensive analysis are hampered by the manual and time-consuming imaging analysis methods applied hitherto. Here, we focus on the early presynaptic formation steps, that is, the presynaptic seeding, initiated by the formation of transient Liprin-a/SYD1 seeding sites, either stabilised or disintegrated over a time span of 30-90 min. Results: To investigate the dynamics of the Liprin-a/SYD1 seeding sites, we developed an automated analysis pipeline for 3D confocal images from in-vivo imaging at distinct time points to analyse fluorescently labelled presynaptic protein dynamics during early synapse formation. The workflow is realised in the data analysis software Amira, utilising the hierarchical watershed algorithm, and was designed for automatic processing with an option for manual proofreading. Compared to the previous 2D manual quantification, this automated approach provides a higher sensitivity in single Liprin-a seeding site detection in low-intensity areas and in regions of dense seeding sites.In addition, it substantially reduces the work time. To account for possible errors occurring in the automated processing, we implemented an additional proofreading step allowing for a manual correction of Liprin-a seeding site segmentation and assignment, thus greatly improving the analysis while only marginally increasing work time by 10% to a total work time reduction of 80% compared to the 2D manual analysis paradigm. Conclusion: The process of synaptogenesis underlies the general principles of locomotion, learning and memory formation. The developed fast and accurate semi-automated 3D workflow provides a substantial progress in the analysis of this molecular process and its application can be easily extended to other dynamic in-vivo research approaches across species. Y1 - 2025 U6 - https://doi.org/10.21203/rs.3.rs-6073150/v1 ER - TY - JOUR A1 - Ngokingha Tchouto, Mireille A1 - Mehl, Julia A1 - Khomeijani Farahani, Saeed A1 - Baum, Daniel A1 - Duda, Georg T1 - Novel image registration approach for combining 2D Osterix and collagen bundles images with 3D µCT JF - Journal of Bone and Mineral Research Y1 - 2026 U6 - https://doi.org/10.1093/jbmrpl/ziag009 VL - 10 IS - 3 ER -